src/jalview/ext/forester/DataConversions.java

   1 package jalview.ext.forester;
   2
   3 import jalview.datamodel.Sequence;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.math.MatrixI;
   6
   7 import org.forester.evoinference.matrix.distance.DistanceMatrix;
   8 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
   9
  10 public final class DataConversions
  11 {
  12   public static org.forester.phylogeny.data.Sequence createForesterSequence(
  13           final SequenceI jalviewSequence, final boolean sequenceIsAligned)
  14   {
  15     org.forester.phylogeny.data.Sequence foresterSeq = new org.forester.phylogeny.data.Sequence();
  16
  17     if (jalviewSequence.getDescription() != null)
  18     {
  19       foresterSeq.setName(jalviewSequence.getDescription());
  20     }
  21
  22     // all tree sequences should be aligned already
  23     foresterSeq.setMolecularSequenceAligned(sequenceIsAligned);
  24
  25     foresterSeq.setMolecularSequence(jalviewSequence.getSequenceAsString());
  26
  27     // add checks for DNA or RNA (infer from forester itself?)
  28     if (jalviewSequence.isProtein())
  29     {
  30       try
  31       {
  32         foresterSeq.setType("protein");
  33       } catch (final PhyloXmlDataFormatException ignore)
  34       {
  35         // do nothing
  36       }
  37
  38     }
  39
  40     return foresterSeq;
  41
  42   }
  43
  44   public static SequenceI createJalviewSequence(
  45           org.forester.phylogeny.data.Sequence foresterSeq)
  46   {
  47     String seq = foresterSeq.getMolecularSequence();
  48     SequenceI jalviewSeq = new Sequence(foresterSeq.getName(), seq, 1,
  49             seq.length() + 1);
  50     return jalviewSeq.deriveSequence();
  51
  52
  53   }
  54
  55
  56   // public static org.forester.phylogeny.data.Accession
  57   // createForesterAccession(
  58   // SequenceI jalviewSequence)
  59   // {
  60   //
  61   //
  62   // org.forester.phylogeny.data.Accession foresterAcs = new
  63   // org.forester.phylogeny.data.Accession();
  64   //
  65   // return foresterAcs;
  66   // }
  67
  68   public static DistanceMatrix createForesterDistanceMatrix(
  69           final MatrixI jalviewInputMatrix,
  70           final String[] matrixIdentifiers)
  71   {
  72
  73     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  74             matrixIdentifiers);
  75     return foresterMatrix;
  76
  77   }
  78
  79   public static DistanceMatrix createForesterDistanceMatrix(
  80           final MatrixI jalviewInputMatrix,
  81           final SequenceI[] matrixSequences)
  82   {
  83     DistanceMatrix foresterMatrix = new ForesterMatrix(jalviewInputMatrix,
  84             matrixSequences);
  85     return foresterMatrix;
  86
  87   }
  88
  89
  90 }